


Don't Tell Mr. Stark

by just_chaotic



Category: Marvel Cinematic Universe
Genre: Alternate Universe - Canon Divergence, Bisexual Peter Parker, Could Be Canon, Fluff and Angst, Infinity War, Nicknames, One Shot, Precious Peter Parker, Tony Stark Needs a Hug, Trans Peter Parker, Whump
Language: English
Status: Completed
Published: 2019-07-16
Updated: 2019-07-16
Packaged: 2020-06-29 09:42:46
Rating: Not Rated
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 1
Words: 3,585
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/19827520
Author URL: https://archiveofourown.org/users/just_chaotic/pseuds/just_chaotic
Summary: A short recounting of how Peter and Tony's relationship changes after the events at Homecoming, and how they became close enough that Tony literally invents time travel after looking at one (1) picture of Peter for about ten seconds. Peter conducts a secretive experiment after he starts getting more comfortable around Tony and the tower. Nothing dangerous or bad, just something he doesn't want to talk about with Tony just yet. Tony does find out, but only after the worst has already happened.





	Don't Tell Mr. Stark

**Author's Note:**

> This is my idea of a one shot between Homecoming and Infinity War (with a glimpse of post-IW, pre-Endgame as well) and I don't know whether to call it canon divergence because I'm not really changing stuff, just adding it in where it wasn't before. I love Irondad/Spiderson and May and Peter being close with Tony and Pepper. This is sweet and torturous and also features my headcanons of trans! and bi!Peter. Enjoy this cute little blurb that I like to think about a lot.

Ever since he had turned down Mr. Stark for the chance to become a full avenger, Peter had to admit that their relationship had gotten much better. He didn’t know if it was a natural progression or a direct result of his supposedly mature decision to stick to helping the little guy. Maybe some combination of both, but no matter what the cause, he and Mr. Stark seemed to be getting… closer? Yeah, closer. 

Like, at first it was just familiarity, and some time actually spent doing “internship” things as the school year went on. They took a picture and made a plaque to make it a little more official, at least to the rest of the workers. Mr. Stark also gave him permission to post the picture on his personal Instagram and Twitter, which Pepper put an indefinite hold on because, “Unfortunately, sweetie, that’s not Tony’s clearance to give. Let me talk to PR and I’ll tell you when you can post it. I do love the bunny ears, though.”

Peter had been on the records as an intern since the beginning but now he actually interacted with the other interns on some research projects, and he spent time with Mr. Stark in his own personal lab. He had made some friends among the other interns, who at first were skeptical of him. Some were even a little hostile, maybe because they didn’t know why a high schooler was suddenly working with them. But after he worked a couple days after school each week for a bit, they learned that he was actually competent, helpful, and most importantly, humble. Peter felt like he was learning a lot, but Mr. Stark said he didn’t give himself enough credit. He thought Peter could lead half the projects and then some, and would have made it so, but Peter kept protesting that he wasn’t ready for that responsibility. Mr. Stark finally relented when Peter pointed out that he would rather spend time in Mr. Stark’s lab anyway, blushing furiously all the while.

After the new year, Pepper actually invited him to dinner. It was awkward at first, both for him and Mr. Stark, because he felt like he was intruding and Mr. Stark felt bad that he hadn’t invited Peter himself. Pepper finally straightened them out with the threat that if they didn’t start acting normal before dessert she would make Friday lock the dishwasher and they would have to wash everything by hand. Things got slightly more normal, Peter talked about school and patrol and Tony poked a little fun at him when he mentioned his newest lego creation with Ned. 

Not long after, weekly dinners on Fridays started to become a thing. Peter was usually there one or two other nights, but by the end of January, May was invited, too and it became a slightly more formal affair. Not that they dressed up or anything, but it was an official plan in all of their schedules. May and Pepper became fast friends, while Peter and Mr. Stark spent more and more time just goofing off or hanging out when they should have been working, and it didn’t bother Peter a bit. Mr. Stark rolled his eyes and groaned at Peter’s “horrible, awful, concerning” brand of humor and Peter even got bold enough to call him out on his dad-jokes a few times. The nicknames had become unbearable. For example: 

“Pull up that blueprint from the other day, kid,” Stark said with a screwdriver in his mouth.

“Which day, Mr. Stark?” Peter asked, looking up from the circuit board he was soldering. Electronics wasn’t typically his thing but Mr. Stark said he only needed practice.

“The day with the one I need, Petey, come on, now,” Mr. Stark mumbled around the screwdriver. He was fiddling with a hologram of the robot they were working on while simultaneously attaching parts to the physical boy, trying to figure out how to best incorporate the gravity manipulation. 

“That’s not helpful, Mr. Stark,” Peter responded with a chuckle.

“Arachnid-Boy, if you’re gonna be my intern, you really have to get better at reading my mind,” he groused back. Peter found the file he was talking about but didn’t cast it up to the hologram yet just to keep the banter going for a minute longer. 

“It’s Spider-Man, Mr. Stark. We’ve been over this.”

“Whatever you say, Speter. Get me that blueprint.”

“What if I called you weird things? Like, ‘here’s your blueprint, metal man’ or stuff like that.”

Tony scoffed. “That’s the best you could come up with, Captain Spandex? _Metal man_?” 

“Well I don’t spend my free time making lists of funny nicknames on my Starkphone notes app,” Peter mumbled with a grin.

“Excuse me? What did you just say, Web Head?” Peter laughed and avoided Mr. Stark's icy (but fake) glare. He cast up the blueprint. The robot was a practice run for a new idea that Peter had for his suit. Even though he could stick in all directions and was certainly strong enough to keep his body aligned to whatever surface, it still felt weird to walk on a vertical wall as if it were a normal floor, because gravity was working in a sideways direction. If they could get this to work, they could upgrade his suit to modify the gravity around him to work with whatever direction he was oriented in.

“I think if you put the circuit board along this area here, Mr. Stark, it lets the machine fit nicely into the main chamber and then gives it the best range. The magnetic field needs to be isolated to the bottom panel, but I still don’t know how to make it adapt to the moving parts.”

“Why don’t you make an Iphone note about it on your dinosaur phone, Prehistoric-Man.” Tony grumbled.

“Yeah, yeah” Peter laughed again. “Let’s get started, Mr. Stank.”

“Don’t make me regret introducing you to Rhodey, Wonder Boy.”

And on it went.

It wasn’t until late February that Peter ventured into one of the labs on his own, though. He had a project he was working on at home but didn’t really have the resources to pull off. Mr. Stark’s personal lab, while amazing, wasn’t the one he needed. This was a chemistry and biology feat, which was not aided by Mr. Starks largely engineering oriented lab. So, he went down to one of the labs that he knew was rarely used, though he didn’t really know why. It was a fine lab, if quite dusty, and Stark Industries did actually have some chemical and bio research happening. Whatever the reason, Peter was glad that the lab and really the whole floor was deserted.

He had told Mr. Stark he was going patrolling, but left his suit at home so that he wasn’t questioned for taking the elevator out of the penthouse. It took a little bit of a fight to insist that he didn’t need a ride home and to let Happy enjoy his Friday night, but Peter managed to escape with a promise that he would text when he got home. He stopped on his desired floor, set a timer with about the average amount of time for a subway trip from Manhattan to Queens, and got to work.

“Fri? Pull up the document ‘Secret Formulas’ from my file ‘Peter’s Chemical X’, please. And don’t tell Mr. Stark I’m here.”

“Document uploaded. And unless your safety is threatened, I can follow that command, Mr. Parker. Would you like me to connect Karen to this room for the duration of your stay?”

“Yeah, Fri, that would be awesome!”

“As you wish,” Friday responded. 

Karen spoke then. “Hi, Peter. Does Mr. Stark know you are in a lab alone?” God. The A.I.’s were conspiring against him. They were really too smart for robots. It was a little scary.

“No, but it’s nothing he needs to worry about. This project is just for me,” Peter said. He sent the text when it was the proper time, and Mr. Stark replied with a thumbs up emoji. As he worked, he talked to Karen to work out the kinks in his process, and she helped him double check his equations. She was also informative about the balance of ingredients he was working with, and took the liberty of suggesting various compounds to neutralize some undesired side-effects. He would have reached the same conclusions eventually, as he found out in the end of his research, but it was a welcome help that she was able to preemptively recognize those solutions. At one point, she requested a blood sample to compare his formula with the compounds in his own blood for compatibility. He didn’t know how to do that until a compartment on the wall opened up with a finger-prick kit. He analyzed the blood and his projected compound, and double checked everything. Twice. 

“I think we did it, Karen.” Peter was exhausted. It was nearly three in the morning. 

“Congratulations, Peter. This formula should be successful with minimal risk and undesired side effects.”

“Thanks, Karen. Now I just need... aha.” Peter found the section of ingredients he was looking for in the atmosphere controlled cases on the wall.

An hour later, he had his compound. Properly bottled, labelled, and packaged, he put it away carefully in his backpack. He put everything away as he found it, and got ready to leave. He was kind of giddy that his whole operation had worked so smoothly. 

“Fri, if I go out the window, will I set off an alarm or anything?”

“No, Mr. Parker, but I would recommend using the elevator instead, seeing as you don’t have your mask with you.”

“Well, not my usual mask, but a mask.” Peter pulled out the old hood from his first suit and put it on. He didn’t notice the loose sheet of paper from his backpack slip out and onto the floor. It was an old homework assignment anyway, and just as he didn’t notice it fall, he wouldn’t notice it missing. He addressed Friday again, “No one will recognize me, it’s too dark to see and hardly anyone will be out this late, and I’ll stick to the less travelled areas, anyway. It’s all good.”

“Whatever you say, Mr. Parker. Do be careful.”

“Always, Friday.” Peter opened the window, slipped on the mask and activated his web shooters, and he was off. 

* * *

~Nearly Two Years Later~

“Your lab hasn’t been touched since… well, it’s been empty. I didn’t go in there after we got back from Sokovia.” Tony and Bruce stood in the elevator as it ascended to Bruce’s old floor. Tony was still wary of Bruce in this form, as much as he hated to admit it. It was just… weird. He knew that made him sound like an ass, but to have the Hulk here with the full awareness and reasoning of Bruce was certainly unsettling.

“I just wanna pack up some stuff and move it to the compound, then you can leave it however you like, Tones.” Bruce sounded almost sad. Nostalgic, maybe. Tony felt slightly nauseous. Coming into the tower always made him feel nauseous nowadays. So, he avoided it at all costs. He avoided the compound, too, to be honest. Too much bad blood there with Steve. Rhodey was the great connector between him and the rest of the Avengers and other heroes. And Bruce and he had reconnected very well after the whole Professor Hulk transformation, despite the physical awkwardness of being in the same space. But they could come to the cabin, whereas him coming to the compound was almost guaranteed to either induce a panic attack or at the very least, an unhealthy amount of anger. And Pepper was trying to help him regulate those emotions better. When she got pregnant, he finally relented and started seeing “that kind of doctor” with a proper recommendation from Bruce and Helen Cho. His counselor wasn’t exactly a fountain of answers, because the world had essentially gone to shit, but he had to admit, working through everything with someone relatively unbiased was helpful. Thankfully Dr. Cho had set him up with someone who knew more than most about superheroes, and thus was informed on his particular situation. 

Tony and Bruce entered the lab, which wasn’t locked. Everything looked as it had been, and they both paused to have a small moment of intense emotion. For Bruce, it was more like reminiscence; for Tony, it was more like regret. He really hated being at the tower. Though this wasn’t his lab, it looked similar enough to drag up memories of Peter. And he preferred to keep those tucked deep inside. Finally, Bruce sighed quietly and moved to start packing. They had brought a few boxes and packed up all the substances safely, along with a few pieces of equipment that were nice enough to warrant transfer to the compound. Other things, like the holo-tables and basic equipment could be left behind, because the compound already had better in the labs there. 

Despite the niceness of Bruce’s lab, their work took less than an hour. As they headed to the door, Bruce turned to take one last look. Tony didn’t feel the urge, but in his hesitation to wait for Bruce, he caught sight of something under one of the tables. A piece of paper. Not important, most likely, but it piqued his curiosity. He set down his one box (next to Bruce’s stack of six) and walked over and picked it up.

Tony hadn’t had a panic attack in a while, but he was certain that was what was happening now. Or perhaps he really was having a heart attack this time. Was that possible with the reactor? Did his heart really beat in the sense that it could stop? Nonetheless, his blood ran cold and his muscles seized. His mind stopped processing reality and all he could see, think, or hear was Peter. His face was suddenly right there in front of him. Laughing. Calling him names or making fun of him for being old. Crying at their first movie night and trying so hard to hide it because he was embarrassed, but not noticing until the last second that Tony was crying, too. Who the hell allowed Coco to be such a sad movie? Tony almost laughed at the thought, the memory, but it came out as more of an insane shriek. Peter’s handwriting stared back at him from the paper, just some inane math problems from whatever calculus lesson he had been in at the time. The writing mocked him, reminded him of the magnitude of his failures and shoved them all right in his face again. 

After a solid few minutes of disassociating and nearly hyperventilating himself into asphyxiation, he finally registered Bruce’s voice and an oxygen mask that had been affixed to his face, dropped from the ceiling by Friday. Like any panic attack, it sucked coming down almost as much as it did during the attack. But he slowly felt his heart rate and breathing slow to normal levels. Surprisingly, Bruce’s touch on his back was comforting and not triggering. He felt the movements of Bruce’s hand that helped him time his breathing.

Bruce seemed prepared to let him leave it alone and not talk about it. But Tony had been doing pretty well in counseling lately, and with Morgan ready to arrive any day, he felt like this was a step he needed to take. Facing these emotions. It was probably unnecessarily triggering and just torturing himself further, but he felt some irrational obligation, like it was the only way he could prove he was a good father. Or, prove that he would be one. Once Morgan was born. Right. 

“Fr-iday,” he gasped. Bruce looked concerned. “Why is Peter’s paper here?”

“Unless Peter’s safety is jeopardized, I cannot answer that, sir,” Friday replied regretfully. 

“Peter is _dead,_ ” Tony whispered harshly. “Anything he asked you to keep from me is officially null and void. Override with whatever code you need, but tell me why the _hell_ his paper is here. He never went in this lab. He worked in my lab with me.”

Friday hesitated for a few beats. “Peter entered this lab on February 27th, 2018. He spent the hours of ten thirty-seven p.m. until four oh-three a.m. in this lab creating a compound of exogenous testosterone for injections, appropriately adjusted to his own metabolism and genetic makeup as different from the average human, due to the effects of his acquisition of superpowers. The compound was successful and safe, checked by both Karen and myself. Peter requested that his presence in this lab not be reported to you, and since his safety was not threatened, I complied.”

Testosterone. He knew that Peter was trans. He knew everything about Peter. When he figured out that Peter was the pajama-clad “Spider-Man” on the internet, he did his research and learned his entire life story. He was sure that Peter knew that he knew, but he would have never pressured him into talking about it if he didn’t want to. Whether that constituted “outing” him or not was a grey area, because, like he said, he was sure that Peter was aware that Tony knew. But because of the grey area, he wouldn’t have ever pushed. When Peter came out to him as bi, Tony almost cried at the closeness he felt, and happiness that Peter trusted him. He loved that kid, as much as he denied it back then. Trying to pass it off as a mentorship, superhero training, or whatever, there was no denying it. He loved Peter. Loves Peter. Present tense. 

He felt a barrage of emotions in the moments following Friday’s confession. Betrayal: did Peter not trust him? He could have helped, or at least supported him while he came up with this. Regret: why didn’t he think about the effects of a super-spider-metabolism on testosterone injections? Surely that would reduce their effectivity. He could have brought it up somehow, not specifically about Peter, but in some way to maybe introduce the idea of working on it together. He had assumed that Peter was on T, but hadn’t ever asked, because he didn’t want to pry or be invasive. He wanted to keep Peter’s trust more than anything else. Sadness: Peter did this without him. He thought they had been getting close at that point. They had been. Peter specifically asked that he not be notified. He lied to him. He remembered that night, now that he thought of it. Peter had said he was patrolling, even sent him a text when he supposedly got home. Guilt: he should have been better for Peter. More resourceful, more thoughtful, someone that Peter could have talked to about these things. Defeat: none of it mattered. Peter was gone. His son, unofficial notwithstanding. He could never change any of this. He would give up almost everything in the world for just that chance. 

Bruce seemed to understand, and just held Tony for a few more minutes. He knew who Peter was, vaguely. Tony never spoke of him, and Pepper cried the few times she did mention him, well out of earshot from Tony. He didn’t know how to help in this situation other than to simply be there, so that’s what he did. When they finally got up, quite a while later, took their boxes and left, Tony had a weird determination in his step. Bruce never really found out what that determination was until he had a conversation with Pepper some weeks later. He couldn’t fit in the house, so they sat on the porch. Pepper held a sleeping baby Morgan while they talked. When he fully explained their day at the tower, Pepper seemed to have an epiphany,

“That must have been the day he put the photo up. I noticed it too, he seemed resolved about something. He told me that night that he loves Peter.” Her eyes got glossy, but she didn’t cry. She seemed determined in a new way, too.

“What did you say to him then?” Bruce asked.

“That we knew. Peter knew. And I loved him too.”

“How did he handle things after that?”

“With that determination you saw in him. Maybe he can’t do anything for Peter, but he doubled down on being a good dad to Morgan. He’s actually napping right now. _Napping_ , Bruce. Because he understands to take sleep when he can get it. He’s never, ever done that for as long as I’ve known him. He goes to counselling and doesn’t complain. He talks to me about what he discusses in counseling. He still doesn’t always know when to stop, but he listens more. For her,” she gestures to the baby, “but also for him.”

“That sounds like Tony. Always reaching for the best.”

“Yeah. That’s him. The best.” The two of them smiled at each other and then at Morgan. Bruce didn’t need to know Peter personally to know that he was the reason this family had such love. And maybe they couldn’t change the way things had gone down. But they could do everything they could now. Morgan would know about Peter. It may be hard now, but Tony and Pepper would both heal, at least enough to tell her about the boy who helped make them a family.


End file.
